Host Protein General Information (ID: PT0349)
  Protein Name
AP endonuclease 1 (APEX1)
  Gene Name
APEX1
  Host Species
Homo sapiens
  Uniprot Entry Name
APEX1_HUMAN
  Protein Families
DNA repair enzymes AP/ExoA family
  EC Number
3.1.-.-
  Subcellular Location
Nucleus
  External Link
NCBI Gene ID
328
Uniprot ID
P27695
Ensembl ID
ENSG00000100823
HGNC ID
HGNC:587
  Function in Host
Multifunctional protein that plays a central role in thecellular response to oxidative stress. The two major activities ofAPEX1 are DNA repair and redox regulation of transcriptional factors. Functions as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in theDNA base excision repair (BER) pathway of DNA lesions induced byoxidative and alkylating agents. Initiates repair of AP sites in DNA bycatalyzing hydrolytic incision of the phosphodiester backboneimmediately adjacent to the damage, generating a single-strand breakwith 5'-deoxyribose phosphate and 3'-hydroxyl ends. Does also incise atAP sites in the DNA strand of DNA/RNA hybrids, single-stranded DNAregions of R-loop structures, and single-stranded RNA molecules. Has a3'-5' exoribonuclease activity on mismatched deoxyribonucleotides atthe 3' termini of nicked or gapped DNA molecules during short-patchBER. Possesses a DNA 3' phosphodiesterase activity capable of removinglesions (such as phosphoglycolate) blocking the 3' side of DNA strandbreaks. May also play a role in the epigenetic regulation of geneexpression by participating in DNA demethylation. Acts as a loadingfactor for POLB onto non-incised AP sites in DNA and stimulates the 5'-terminal deoxyribose 5'-phosphate (dRp) excision activity of POLB. Plays a role in the protection from granzymes-mediated cellular repairleading to cell death. Also involved in the DNA cleavage step of classswitch recombination (CSR). On the other hand, APEX1 also exertsreversible nuclear redox activity to regulate DNA binding affinity andtranscriptional activity of transcriptional factors by controlling theredox status of their DNA-binding domain, such as the FOS/JUN AP-1complex after exposure to IR. Involved in calcium-dependent down-regulation of parathyroid hormone (PTH) expression by binding tonegative calcium response elements (nCaREs). Together with HNRNPL orthe dimer XRCC5/XRCC6, associates with nCaRE, acting as an activator oftranscriptional repression. Stimulates the YBX1-mediated MDR1 promoteractivity, when acetylated at Lys-6 and Lys-7, leading to drugresistance. Acts also as an endoribonuclease involved in the control ofsingle-stranded RNA metabolism. Plays a role in regulating MYC mRNAturnover by preferentially cleaving in between UA and CA dinucleotidesof the MYC coding region determinant (CRD). In association with NMD1, plays a role in the rRNA quality control process during cell cycleprogression. Associates, together with YBX1, on the MDR1 promoter. Together with NPM1, associates with rRNA. Binds DNA and RNA. [1-25]
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  Related KEGG Pathway
Base excision repair hsa03410            Pathway Map 
  3D Structure

Function of This Protein During Virus Infection
Virus NameSARS-COV-2 Protein Function Anti-viral [26]
Infected TissueLung Infection Time7-9 Days
Infected CellCalu-3 Cells (Human epithelial cell line) Cellosaurus IDCVCL_0609 
Method DescriptionTo detect the role of host protein APEX1 in viral infection, APEX1 protein knockout Calu-3 Cells were infected with SARS-COV-2 for 7 - 9 Days , and the effects on infection was detected through CRISPR-based genome-wide gene-knockout screen.
ResultsIt is reported that knockout of APEX1 increases SARS-CoV-2 RNA levels compared with control group.

 Full List of Virus RNA Interacting with This Protien
            RNA Region: Not Specified Virus Region (hCoV-19/USA/WA1/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [27]
              Strains Name
hCoV-19/USA/WA1/2020
              Strains Family
Alpha (B.1.1.7)
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7.5 cells (Hepatocyte derived cellular carcinoma cell)  (CVCL_7927 )
              Cell Originated Tissue Liver
              Infection Time 48 h
              Interaction Score FDR ≤ 0.05
              Method Description comprehensive identification of RNA-binding proteins by massspectrometry (ChIRP-MS)

Differential Gene Expression During SARS-COV-2 Infection
GEO Accession: GSE152641
Sample Type: Blood
Samples Details: Healthy Control: 24; COVID-19: 62
Platform: GPL24676 Illumina NovaSeq 6000
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GEO Accession: GSE162835
Sample Type: Nasopharyngeal Swabs
Samples Details: COVID-19 (Mild Symptoms): 37; COVID-19 (Moderate Symptoms): 10; COVID-19 (Severe Symptoms): 3
Platform: GPL24676 Illumina NovaSeq 6000
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GEO Accession: GSE175779
Sample Type: Human Bronchial Epithelial Cells
Samples Details: Healthy Control: 4 (0, 24, 48, 72 and 96 h); COVID-19: 4 (24, 48, 72 and 96 h)
Platform: GPL18573 Illumina NextSeq 500
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Potential Drug(s) that Targets This Protein
Drug Name DrunkBank ID Pubchem ID TTD ID REF
Iucanthone DB04967  10180  D09OZC  [27]

Protein Sequence Information
MPKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
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References
1 Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell. 2011 Apr 29;145(3):423-34.
2 APE1/Ref-1 interacts with NPM1 within nucleoli and plays a role in the rRNA quality control process. Mol Cell Biol. 2009 Apr;29(7):1834-54.
3 Human AP-endonuclease 1 and hnRNP-L interact with a nCaRE-like repressor element in the AP-endonuclease 1 promoter. Nucleic Acids Res. 2002 Feb 1;30(3):823-9.
4 The interaction between Ku antigen and REF1 protein mediates negative gene regulation by extracellular calcium. J Biol Chem. 1996 Apr 12;271(15):8593-8.
5 Isolation of cDNA clones encoding a human apurinic/apyrimidinic endonuclease that corrects DNA repair and mutagenesis defects in E coli xth (exonuclease III) mutants. Nucleic Acids Res. 1991 Oct 25;19(20):5519-23.
6 Characterization of the endoribonuclease active site of human apurinic/apyrimidinic endonuclease 1. J Mol Biol. 2011 Sep 2;411(5):960-71.
7 SIRT1 deacetylates APE1 and regulates cellular base excision repair. Nucleic Acids Res. 2010 Jan;38(3):832-45.
8 Critical lysine residues within the overlooked N-terminal domain of human APE1 regulate its biological functions. Nucleic Acids Res. 2010 Dec;38(22):8239-56.
9 Identification of Apurinic/apyrimidinic endonuclease 1 (APE1) as the endoribonuclease that cleaves c-myc mRNA. Nucleic Acids Res. 2009 Jul;37(12):3946-58.
10 Characterization of abasic endonuclease activity of human Ape1 on alternative substrates, as well as effects of ATP and sequence context on AP site incision. J Mol Biol. 2008 May 23;379(1):17-27.
11 Regulatory role of human AP-endonuclease (APE1/Ref-1) in YB-1-mediated activation of the multidrug resistance gene MDR1. Mol Cell Biol. 2008 Dec;28(23):7066-80.
12 Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease. Mutat Res. 2008 Aug 25;643(1-2):54-63.
13 Granzyme K degrades the redox/DNA repair enzyme Ape1 to trigger oxidative stress of target cells leading to cytotoxicity. Mol Immunol. 2008 Apr;45(8):2225-35.
14 Identification and characterization of mitochondrial abasic (AP)-endonuclease in mammalian cells. Nucleic Acids Res. 2006 Apr 14;34(7):2067-76.
15 Cleaving the oxidative repair protein Ape1 enhances cell death mediated by granzyme A. Nat Immunol. 2003 Feb;4(2):145-53.
16 An exonucleolytic activity of human apurinic/apyrimidinic endonuclease on 3 mispaired DNA. Nature. 2002 Feb 7;415(6872):655-9.
17 Activation of APE/Ref-1 redox activity is mediated by reactive oxygen species and PKC phosphorylation. Nucleic Acids Res. 2001 Jul 15;29(14):3116-22.
18 Thioredoxin nuclear translocation and interaction with redox factor-1 activates the activator protein-1 transcription factor in response to ionizing radiation. Cancer Res. 2000 Dec 1;60(23):6688-95.
19 Phosphorylation of the DNA repair protein APE/REF-1 by CKII affects redox regulation of AP-1. Oncogene. 1999 Jan 28;18(4):1033-40.
20 Rapid dissociation of human apurinic endonuclease (Ape1) from incised DNA induced by magnesium. J Biol Chem. 1998 Nov 13;273(46):30360-5.
21 Activation of apurinic/apyrimidinic endonuclease in human cells by reactive oxygen species and its correlation with their adaptive response to genotoxicity of free radicals. Proc Natl Acad Sci USA. 1998 Apr 28;95(9):5061-6.
22 Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway. Proc Natl Acad Sci USA. 1997 Jul 8;94(14):7166-9.
23 AP-1 transcriptional activity is regulated by a direct association between thioredoxin and Ref-1. Proc Natl Acad Sci USA. 1997 Apr 15;94(8):3633-8.
24 Asparagine 212 is essential for abasic site recognition by the human DNA repair endonuclease HAP1. Nucleic Acids Res. 1996 Nov 1;24(21):4217-21.
25 Identification of residues in the human DNA repair enzyme HAP1 (Ref-1) that are essential for redox regulation of Jun DNA binding. Mol Cell Biol. 1993 Sep;13(9):5370-6.
26 Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2. Nat Commun. 2022 Apr 25;13(1):2237.
27 Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions. Cell. 2021 Apr 29;184(9):2394-2411.e16.